On 5 January 2009 the Israeli army rounded up around 65 Palestinians (including 11 women and 11 children under the age of 14) in Gaza, several of whom were waving white flags. After handcuffing the men and stripping them to their underwear, the soldiers marched their captives 2km north to al-Atatra and ordered them to climb into three pits, each three metres high and surrounded by barbed wire. The prisoners were forced to sit in stress positions, leaning forward with their heads down, and prohibited from talking to one another. On their first day they were denied food and water. On the second and third, each was given a sip of water and a single olive. On the fourth day the women and children were released and the men were transferred to military barracks.

It was just one of the stories to emerge from the UN fact-finding mission on the Gaza conflict conducted by the South African jurist Richard Goldstone. The report accused Israel and Hamas of committing war crimes and "possibly" crimes against humanity. But in a conflict that saw 10 Israeli soldiers and three civilians killed compared with about 1,400 Gazans, Goldstone was particularly scathing about Israel's "deliberately disproportionate attack designed to punish, humiliate and terrorise a civilian population" – which he said amounted to "collective punishment".

The Israeli government and the pro-Israel lobbies concentrated their displeasure not on the substance of Goldstone's report but the essence of his identity. Branded a "self-hating Jew", he was effectively barred from his grandson's bar mitzvah after the South African Zionist Federation threatened to picket it. The prominent US constitutional lawyer Alan Dershowitz has described Goldstone as a "despicable human being", "an evil, evil man", "a traitor to the Jewish people" and the UN's "token court Jew".

Then this month came "revelations" from an Israeli newspaper that, as a judge under the apartheid regime, Goldstone sentenced black people to death. This, according to Israel's government, discredits not only Goldstone but everything he discovered about Gaza and, by association, international criticism of the occupation. "Such a person should not be allowed to lecture a democratic state defending itself against terrorists, who are not subject to the criteria of international moral norms," argued the Knesset Speaker, Reuven Rivlin.

"Although he was involved in clear racist activity, he had no problem writing such a report," said the chairman of the Knesset's state control committee, Yoel Hasson, who called Goldstone a hypocrite. Not to be outdone, Dershowitz (a strident advocate of torture) has now likened Goldstone to the Nazi geneticist Josef Mengele.

This crude one-downmanship in identity politics has no winners and many losers. Facts about racism in the past cannot excuse realities about racism in the present. Playing off the legacy of South Africa's townships against the plight of the captives of al-Atatra seeks not to alleviate the suffering of either group but in effect to dismiss them. But for all the hyperbole and absurdity, there are important principles at stake about who can claim moral authority, on what basis, and to what end.

Let's start with the most obvious. This is a cynical ploy by the Israeli government to divert attention from the findings of the UN report. Government officials have almost said as much. A foreign ministry official described the investigation by the Israeli newspaper Yedioth Ahronoth as "explosive PR material". Hasson claims: "Had [the Israeli foreign ministry discovered this earlier], it would have greatly helped us in our activity against the report." But the report is about Gaza, not Goldstone. Having lost control of the message, Israel is now trying to shoot the messenger.

That Israel would try to do so on the backs of black South Africans is a laughable indication of its desperation. For if Goldstone was complicit in apartheid's crimes, then Israel was far more so. Israel was South Africa's principal and most dependable arms dealer. As we learn elsewhere in the Guardian today, it even offered to sell the South African regime nuclear weapons.

"Throughout the 70s and 80s Israel had a deep, intimate and lucrative relationship with South Africa," explains Sasha Polakow-Suransky, author of The Unspoken Alliance: Israel's Secret Relationship With Apartheid South Africa. "Israel's arms supplies helped to prolong the apartheid regime's rule and to survive international sanctions." No criticism of Goldstone's complicity from representatives of the Israeli state can be taken seriously that does not acknowledge and condemn Israel's even greater support of the self-same system.

But just because the Israeli government wants to change the subject doesn't mean that we have to. Goldstone's apartheid record matters. For the left to claim it doesn't, simply because he came up with a conclusion about Gaza that they agree with, would also be cynical. Appointed senior counsel in 1976, the year of the Soweto uprising, Goldstone rose through the South African judiciary during one of apartheid's most vicious periods. While in power he ordered the execution of two black South Africans and turned down the appeals of many others.

"A historian who finds excuses for such conduct by references to the supposed spirit of the times or by omission or by silence," wrote the late Trinidadian intellectual CLR James in The Black Jacobins, "shows thereby that his account of events is not to be trusted."

Goldstone's claim that faced with a "moral dilemma" he thought "it was better to fight from inside than not at all", is inadequate. Not only did he uphold apartheid laws, he enforced them. This is not a question of 20:20 hindsight: many in a similar position at that time chose a more principled stand. Both morally and professionally he had other options, and he is compromised by not having taken them.

But his record did not end with apartheid. While he may not have led the drive to a non-racial democracy, he followed it eagerly. When the system started to collapse, he fully embraced change. Nelson Mandela asked him to chair the commission into public violence primarily because he was trusted by both sides. As such, he was an archetypical transitional figure. After that he went on to produce respected reports into the ethnic conflicts in Rwanda and Yugoslavia. So while his credibility as a human rights advocate might be diminished, it is by no means destroyed.

Finally, there is the insidious role that Israel has attempted to play as ideological gatekeeper for acceptable political behaviour among Jews. The attempt to tarnish any criticism of Israel, regardless of its merits, as unjust is untenable; to castigate them as un-Jewish is deplorable. "What saddens me today is that any Jew who speaks out with an independent voice, especially with the conduct of the state of Israel, is regarded as a self-hating Jew," says retired South African constitutional court justice Albie Sachs, who is also Jewish. "Why should someone be made to choose between being a Jew and having a conscience?"

Gary Younge's book Who Are We – and Should It Matter in the 21st Century? is published on 3 June

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• This article was amended on 24 May 2010. The original described Abie Sachs as a retired supreme court justice. This has been corrected.